Wiki source code of The Virtual Brain In Clinical Research August 2022
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| 1 | == == | ||
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| 3 | [[image:VirtualBrainClinicalResearch.png]] | ||
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| 5 | == **Week 7 “The Virtual Brain and multiscale co-simulation” – Dr. Dionysios Perdikis** == | ||
| 6 | |||
| 7 | August 9th, 2022 | ||
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| 9 | |||
| 10 | === Recommendation for self-study === | ||
| 11 | |||
| 12 | * [[TVB advanced tutorials>>https://training.incf.org/course/virtual-brain-node-6-workshop]] | ||
| 13 | * [[Schirner, Domide, Perdikis, Triebkorn, Stefanovski, Pai, Prodan, Valean, Palmer, Langford, Blickensdörfer, van der Vlag, Diaz-Pier, Peyser, Woodman, Zehl, Fousek, Petkoski, Kusch, Hashemi, Marinazzo, Mangin, Flöel, Akintoye, Stahl, Deco, McIntosh, Hilgetag, Morgan, Schuller, Upton, McMurtrie, Dickscheid, Bjaalie, Amunts, Mersmann, Jirsa, Ritter (2022). Brain Simulation as a Cloud Service: The Virtual Brain on the European Research Platform EBRAINS. Neuroimage>>https://www.sciencedirect.com/science/article/pii/S1053811922001021]] | ||
| 14 | * ((( | ||
| 15 | [[Sanz-Leon, P., Knock, S. A., Spiegler, A., & Jirsa, V. K. (2015). Mathematical framework for large-scale brain network modeling in The Virtual Brain. Neuroimage>>https://www.sciencedirect.com/science/article/pii/S1053811915000051]] | ||
| 16 | ))) | ||
| 17 | |||
| 18 | |||
| 19 | === What can I find here? === | ||
| 20 | |||
| 21 | * Presentation slides from the course's lecture. | ||
| 22 | * The notebook ([[SimulateWithEBRAINS.zip>>attach:SimulateWithEBRAINS.zip]]) demonstrated during the workshop. | ||
| 23 | |||
| 24 | |||
| 25 | === Guide to run the use-case notebook === | ||
| 26 | |||
| 27 | 1. Run the EBRAINS TVB-Multiscale app by browsing to [[https:~~/~~/tvb-multiscale.apps.hbp.eu/>>https://tvb-multiscale.apps.hbp.eu/]] and logging in with your EBRAINS account. (The first time you log-in, you might need to try several times by refreshing the page, until it works for you!) | ||
| 28 | 1. Navigate to "Contributed-Notebooks" folder, which offers user-specific persistent storage. | ||
| 29 | 1. Upload and unzip there [[SimulateWithEBRAINS.zip>>attach:SimulateWithEBRAINS.zip]] by starting a terminal session or a new notebook and running unzip SimulateWithEBRAINS.zip | ||
| 30 | 1. Run the TVB-corr-cortex-opt.ipynb notebook for TVB-ANNarchy cosimulation and the ANNarchy-spiking-cortex.ipynb one for ANNarchy only simulation. | ||
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| 32 | == == |